Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence?

Microbial metabolic enzymes, pathways and microbial hosts for co-metabolic degradation of organic micropollutants in wastewater

Organic micropollutants (OMPs) in wastewater present significant environmental challenges, but effective removal strategies are hindered by our limited understanding of their co-metabolic biodegradation. We aim to elucidate the microbial enzymes, metabolic pathways, and community members involved in OMP co-metabolic degradation, thereby paving the way for more effective wastewater treatment strategies. We integrated multi-omics (metagenomics, metaproteomics, and metabolomics) and functional group analysis to investigate 24 OMPs under three aeration conditions. Our findings reveal that oxidoreductases, particularly cytochrome P450s and peroxidases, are crucial for recalcitrant OMPs containing halogen groups (-Cl, -F) like fluoxetine and diuron. Hydrolases, including amidases, are instrumental in targeting amide-containing (-CONH₂) OMPs such as bezafibrate and carbamazepine. Regarding microbial metabolism involved in OMP co-metabolic degradation, we found that amino acid metabolism is crucial for degrading amine-containing (-NH₂) OMPs like metoprolol and citalopram. Lipid metabolism, particularly for fatty acids, contributes to the degradation of carboxylic acid (-COOH) containing OMPs such as bezafibrate and naproxen. Finally, with Actinobacteria, Bacteroidetes, and Proteobacteria emerging as primary contributors to these functionalities, we established connections between OMP functional groups, degradation enzymes, metabolic pathways, and microbial phyla. Our findings provide generalized insights into structure-function relationships in OMP co-metabolic degradation, offering the potential for improved wastewater treatment strategies.

Presence of Micropollutants and Transformation Products During Subsurface Irrigation with Treated Wastewater Assessed by Non-Target Screening Analysis

While wastewater treatment plant (WWTP) effluent offers a potential alternative source for irrigation, the fate of organic micropollutants (OMPs), including transformation products (TPs), in effluent-irrigated fields remains largely unknown. Using non-target analysis (NTA), we investigated OMPs in WWTP effluent and their distribution throughout a full-scale subsurface irrigation (SSI) field where effluent was used for irrigation. Our results indicate that TPs accounted for approximately 80% of the detected effluent OMPs. Weather and SSI hydrology seem to influence OMP distribution and transformation. Wetter conditions promoted deeper leaching of OMPs in soil, and drier conditions favored their capillary rise and biotransformation, as shown by the detection of 37% more TPs in the rhizons during a dry year. On average 45 OMPs, at least 50% with a logD <3, were detected at -2.3 m depth, highlighting their potential to reach groundwater and the importance of including TPs in further risk assessment. This approach demonstrates how NTA and subsequent data analysis tools can support the identification of (unknown) OMPs and contribute to understanding OMP fate under field conditions, which is the first step in an exposure-driven environmental risk assessment. Overall, our study emphasizes the importance of carefully considering (unknown) OMPs for more responsible effluent reuse.

Insights from multiple stable isotopes (C, N, Cl) into the photodegradation of herbicides atrazine and metolachlor

Many processes can contribute to the attenuation of the frequently detected and toxic herbicides atrazine and metolachlor in surface water, including photodegradation. Multi-element compound-specific isotope analysis has the potential to decipher between these different degradation pathways as Cl is a promising tool for both pathway identification and a sensitive indicator of degradation for both atrazine and metolachlor. In this study, photodegradation experiments of atrazine and metolachlor were conducted under simulated sunlight in buffered solutions (direct photodegradation) and with nitrate (indirect photodegradation by OH radicals) to determine kinetics, transformation products and isotope fractionation for C, N and for the first time Cl. For metolachlor, the C-Cl dual isotope slope (ΛC/Cl = 0.46 ± 0.19) is identical to previously reported values for hydrolysis and biodegradation in soils, suggesting the same reaction mechanism (C-Cl bond breakage by SN2 nucleophilic substitution). For atrazine, both direct and indirect photodegradation resulted in a pronounced inverse isotope effect for chlorine (εCl = 6.9 ± 3.3 ‰, and εCl = 2.3 ± 1.2 ‰, respectively), leading to characteristic dual isotope slopes (ΛC/Cl = -0.49 ± 0.17 and ΛC/Cl = -0.31 ± 0.10, respectively). These values are distinct from those previously reported for abiotic hydrolysis, biotic hydrolysis and oxidative dealkylation which are all relevant processes in surface water, opening the path for pathway identification in future field studies.

Fitness and adaptive evolution of a Rhodococcus sp. harboring dioxin-catabolic plasmids

Catabolic plasmids are critical factors in the degradation of recalcitrant xenobiotics, such as dioxins. Understanding the persistence and evolution of native catabolic plasmids is pivotal for controlling their function in microbial remediation. Here, we track the fitness and evolution of Rhodococcus sp. strain p52 harboring dioxin-catabolic plasmids under nonselective conditions without contaminant. Growth curve analysis and competition experiments demonstrated that pDF01 imposed fitness costs, whereas pDF02 conferred fitness benefits. During stability tests, pDF01 tended to be lost from the population, while pDF02 maintained at least one copy in the cell until proliferation of the 400th generation. Genome-wide gene expression profiling combined with codon usage bias analysis revealed that the high expression of pDF01 genes involved in dibenzofuran catabolism and regulation caused metabolic burdens. In contrast, potential cooperation between the pDF02-encoded short-chain dehydrogenase/reductase family oxidoreductase and the redox cofactor mycofactocin, which synthetic genes are located on the chromosome, may explain the benefit of pDF02. The fitness cost imposed by pDF01 was alleviated during adaptive evolution and was associated with the transcriptional downregulation of the dibenzofuran degradation genes on pDF01, and the global regulation of genome-wide gene expression involving basic metabolism, transport, and signal transduction. This study broadens our understandings on the persistence and evolution of dioxin-catabolic mega-plasmids, thus paving the way for the bioremediation of recalcitrant xenobiotic pollution in the environment.

Broad Microbial Community Functions in a Conventional Activated Sludge System Exhibit Temporal Stability

Wastewater microbial communities within conventional activated sludge (CAS) systems can perform hundreds of biotransformations whose relative importance, frequency, and temporal stability remain largely unexplored. To improve our understanding of biotransformations in CAS systems, we collected 24 h composite samples from the influent and effluent of a CAS system over 14 days, analyzed samples using high-resolution mass spectrometry (HRMS), and conducted a nontarget analysis of our HRMS acquisitions. We found that over 50% of the chemical features in the influent were completely removed, and the daily number of detected features exhibited low variability with a coefficient of variation of 0.07. Additionally, we found 352 Core chemical features present in every sample at both locations. We used chemical features to search for evidence of 19 potential biotransformations and detected 9 of these biotransformations at a frequency of over 80 times per day, where evidence for dehydrogenations, hydroxylations, and acetylations was most frequently detected. The daily number of detections for the 9 biotransformations exhibited coefficients of variation ranging from 0.13-0.20, revealing the broad temporal stability for these wastewater microbial community functions. This stability contrasts with the previously observed temporal variability for micropollutant biotransformations, suggesting that micropollutant biotransformations are linked to specialized microbial community functions.

Bacterial community and dissolved organic matter networks in urban river: The role of human influence

Human activities have significantly altered the biogeochemical cycles of carbon, nitrogen, and sulfur in aquatic ecosystems, leading to ecological problems.This study utilized 16S rRNA gene high-throughput sequencing and excitation-emission matrix parallel factor analysis (EEM-PARAFAC) to evaluate the bacterial community composition and dissolved organic matter structure in the upstream (less impacted) and downstream (severely impacted) sections of the river, with a focus on the interactions between bacterial diversity and dissolved organic matter (DOM) characteristics.Results indicated significant spatial diversity in bacterial communities, with a higher α-diversity upstream compared to the more polluted downstream sections. Environmental parameters, particularly total phosphorus (TP) and dissolved oxygen (DO), were found to significantly influence the distribution and composition of bacterial phyla through redundancy analysis. The pattern of bacterial community assembly has shifted from predominantly deterministic to predominantly stochastic as a result of human activities. The analysis of DOM through EEM-PARAFAC identified three main fluorescent components, reflecting varied sources and interactions with bacterial communities. Upstream, microbial activities predominantly contributed to autochthonous DOM, while downstream, increased inputs of allochthonous DOM from human activities were evident. Furthermore, the study revealed that through the introduction of various organic pollutants and nutrient loads that shift microbial metabolic functions towards increased degradation and transformation of complex organic compounds downstream. Structural equation modeling (SEM) revealed that upstream human activities primarily affected bacterial communities indirectly by altering DOM properties. In contrast, downstream activities had both direct and indirect effects due to higher pollutant loads and more complex environmental conditions. These interactions underline the profound effect of anthropogenic factors on riverine ecosystems and emphasize the importance of managing human impacts to preserve microbial biodiversity and water quality.

Variability of Biodegradation Rates of Commercial Chemicals in Rivers in Different Regions of Europe

Biodegradation is one of the most important processes influencing the fate of organic contaminants in the environment. Quantitative understanding of the spatial variability in environmental biodegradation is still largely uncharted territory. Here, we conducted modified OECD 309 tests to determine first-order biodegradation rate constants for 97 compounds in 18 freshwater river segments in five European countries: Sweden, Germany, Switzerland, Spain, and Greece. All but two of the compounds showed significant spatial variability in rate constants across European rivers (ANOVA, P < 0.05). The median standard deviation of the biodegradation rate constant between rivers was a factor of 3. The spatial variability was similar between pristine and contaminated river segments. The longitude, total organic carbon, and clay content of sediment were the three most significant explanatory variables for the spatial variability (redundancy analysis, P < 0.05). Similarities in the spatial pattern of biodegradation rates were observed for some groups of compounds sharing a given functional group. The pronounced spatial variability presents challenges for the use of biodegradation simulation tests to assess chemical persistence. To reflect the variability in the biodegradation rate, the modified OECD 309 test would have to be repeated with water and sediment from multiple sites.

Modulation of irrigation-induced microbial nitrogen‑iron redox to per- and polyfluoroalkyl substances' water-soil interface release in paddy fields: Activation or immobilization?

Understanding the modulation of paddy field irrigation to the migration of per- and polyfluoroalkyl substances (PFAS) at the water-soil interface is pivotal for the management of PFAS pollution in paddy soil and surrounding surface water environments. In flooded soils, soil organic matter was transformed into aromatic protein-like dissolved organic matter (DOM). Meanwhile, Na+, K+, and Mg2+ were translocated into extracellular polymeric substances (EPS) under the catalysis of cation channel enzymes (p < 0.05), provided ion bridging for the binding of DOM and PFAS, and accelerated the accumulation of C4-C9 PFAS in overlying water (41.79-99.14 %). Short-chain PFAS's accumulation in soil solution of drought soils was stimulated by microorganisms secreting soluble microbial by-product-like DOM (53.15-97.96 %). Furthermore, PFAS's distribution in flood soils was dominated by bacterial denitrification and iron-reduction, whereas iron-oxidation and ammoxidation controlled that in drought soils. The transformation of organic carbon including CO and COC caused by irrigation-induced redox modulated PFAS cross-media translocation. Iron‑nitrogen redox in flooded paddy soils immobilized the PFAS's migration into overlying water (p < 0.05). Our findings have profound implications for PFAS's pollution control, surface water environmental protection, and rice production security in paddy fields.

Enhancing biodegradation of vegetable oil-contaminated soil with soybean texturized waste, spent mushroom substrate, and stabilized poultry litter in microcosm systems

Industrial activities contribute to environmental pollution, particularly through unregulated effluent discharges, causing adverse effects on ecosystems. Vegetable oils, as insoluble substances, exacerbate this pollution, forming impermeable films and affecting the oxygen transfer, leading to serious habitat disruption. Organic wastes, such as soybean texturized waste, spent mushroom substrate, and stabilized poultry litter, were assessed for their efficacy in enhancing the degradation of vegetable oil in contaminated soil. For this purpose, contaminated soil was amended with each of the wastes (10% w/w) using microcosm systems, which were monitored physico-chemically, microbiologically and toxicologically. Results indicate that the wastes promoted significant oil degradation, achieving 83.1, 90.7, and 86.2% removal for soybean texturized waste, spent mushroom substrate, and stabilized poultry litter, respectively, within a 90-day period. Additionally, they positively influenced soil microbial activity, as evidenced by increased levels of culturable microorganisms and hydrolytic microbial activity. While bioassays indicated no phytotoxicity in most cases, soybean texturized waste exhibited inhibitory effects on seed germination and root elongation of Lactuca sativa. This study significantly enhances our comprehension of remediation techniques for sites tainted with vegetable oils, highlighting the critical role of organic waste as eco-friendly agents in soil restoration. Emphasizing the practical implications of these findings is imperative to underscore the relevance and urgency of addressing vegetable oil contamination in soil. Moving forward, tailored strategies considering both contaminant characteristics and soil ecosystem traits are vital for ensuring effective and sustainable soil remediation.

Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater

Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.

Microalgal multiomics-based approaches in bioremediation of hazardous contaminants

The enhanced industrial growth and higher living standards owing to the incessant population growth have caused heightened production of various chemicals in different manufacturing sectors globally, resulting in pollution of aquatic systems and soil with hazardous chemical contaminants. The bioremediation of such hazardous pollutants through microalgal processes is a viable and sustainable approach. Accomplishing microalgal-based bioremediation of polluted wastewater requires a comprehensive understanding of microalgal metabolic and physiological dynamics. Microalgae-bacterial consortia have emerged as a sustainable agent for synergistic bioremediation and metabolite production. Effective bioremediation involves proper consortium functioning and dynamics. The present review highlights the mechanistic processes employed through microalgae in reducing contaminants present in wastewater. It discusses the multi-omics approaches and their advantages in understanding the biological processes, monitoring, and dynamics among the partners in consortium through metagenomics. Transcriptomics, proteomics, and metabolomics enable an understanding of microalgal cell response toward the contaminants in the wastewater. Finally, the challenges and future research endeavors are summarised to provide an outlook on microalgae-based bioremediation.

Seasonal variation and dissolved organic matter influence on the distribution, transformation, and environmental risk of pharmaceuticals and personal care products in coastal zone: A case study of Tianjin, China

Pharmaceuticals and personal care products (PPCPs) are emerging contaminants that have raised urgent environmental issues. The dissolved organic matter (DOM) plays a pivotal role on PPCPs' migration and transformation. To obtain a comprehensive understanding of the occurrence and distribution of PPCPs, a seasonal sampling focused on the riverine system in coastal zone, Tianjin, Bohai Rim was conducted. The distribution and transformation of thirty-three PPCPs and their interaction with DOM were investigated, and their sources and ecological risks were further evaluated. The total concentration of PPCPs ranges from 0.01 to 197.20 μg/L, and such value is affected by regional temperature, DOM and land use types. PPCPs migration at soil-water interface is controlled by temperature, sunlight, water flow and DOM. PPCPs have a high affinity to the protein-like DOM, while the humus-like DOM plays a negative influence and facilitates PPCPs' degradation. It is also found that protein-like DOM can represent point source pollution, while humus-like substances indicate non-point source (NPS) emission. Specific PPCPs can be used as markers to trace the source of domestic discharge. Additionally, daily use PPCPs such as ketoprofen, caffeine and iopromide are estimated to be the main risk substances, and their ecological risk varies on space, season and river hydraulic condition.

Persistence of microbiological hazards in food and feed production and processing environments

Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Combining large-scale investigation and quantum chemical calculation of pharmaceuticals: Spatiotemporal patterns of occurrence and structural insights into removal

This study investigated the spatiotemporal distribution of 17 pharmaceuticals in wastewater treatment plants (WWTPs) from 17 provinces across China, and explored structural insights into their removal in full-scale wastewater treatment processes by quantum chemistry. Briefly, 10 pharmaceuticals were detected in above 85 % of samples, of which ibuprofen and sulfamethoxazole dominated with concentrations up to the μg/L level. Seasonally, concentrations of psychoactive drugs (PDs) were 1.3-2.6 times higher in summer than in other seasons. Spatially, higher average concentrations were detected in northern WWTPs, and regions with similar economic levels exhibited similar contamination patterns. Pharmaceutical removal in WWTPs ranged from 41.4 % (carbamazepine) to 87.2 % (sulfamethizole), with the secondary treatment segment, especially aerobic treatment units, maintaining an important position. Molecular structural mechanisms behind these removal performances were further revealed. Firstly, we demonstrated a significant association of pharmaceutical overall removal with electrophilicity index (ωcubic) as well as the lowest unoccupied molecular orbital energy (ELUMO). Highly electrophilic pharmaceuticals may persist in WWTPs and their sensitivity to electron exchange reactions accounted for the discrepant removal. In terms of treatment segments, pharmaceuticals with reaction sites masked in molecular structure, such as ibuprofen and venlafaxine, showed a propensity for tertiary treatment suitability. Furthermore, enzymes of aerobic units exhibited excellent docking affinity to pharmaceutical molecules with an average affinity of -7.2 kcal/mol, and hydrogen-bond interactions played an important factor in promoting biodegradation. Our results emphasize the necessity of assessing pharmaceutical contamination on a larger spatiotemporal scale. Moreover, the structural insights into removal phenomena offer scientific molecular-level justification for the design and optimization of pharmaceutical treatment technologies in WWTPs.

Bioremediation of an industrial soil contaminated by hydrocarbons in microcosm system, involving bioprocesses utilizing co-products and agro-industrial wastes

The present study describes practical implication of bioaugmentation and biostimulation processes for bioremediation of an industrial soil chronically contaminated by hydrocarbons. For this purpose, biomass production of six autochthonous hydrocarbon-degrading bacteria were evaluated as inoculum of bioaugmentation strategy, by testing carbon and nitrogen sources included co-products and agro-industrial waste as sustainable and low-cost components of the growth medium. Otherwise, biostimulation was approached by the addition of optimized concentration of nitrogen and phosphorus. Microcosm assays showed that total hydrocarbons (TH) were significantly removed from chronically contaminated soil undergoing bioremediation treatment. Systems Mix (bioaugmentation); N,P (biostimulation) and Mix + N,P (bioaugmentation and biostimulation) reached higher TH removal, being 89.85%, 91.00%, 93.04%, respectively, comparing to 77.83% of system C (natural attenuation) at 90 days. The increased heterotrophic aerobic bacteria and hydrocarbon degrading bacteria counts were according to TH biodegrading process during the experiments. Our results showed that biostimulation with nutrients represent a valuable alternative tool to treat a chronically hydrocarbon-contaminated industrial soil, while bioaugmentation with a consortium of hydrocarbon degrading bacteria would be justified when the soil has a low amount of endogenous degrading microorganisms. Furthermore, the production of inoculum for application in bioaugmentation using low-cost substrates, such as industrial waste, would lead to the development of an environmentally friendly and attractive process in terms of cost-benefit.

Assessment of the Presence of Transformation Products of Certain Pharmaceutical Products (Psychotropic Family) by Suspect and Non-Targeted HRMS Screening in Wastewater Treatment Plants

Aquatic environments are the final receptors of human emissions and are therefore contaminated by molecules, such as pharmaceuticals. After use, these compounds and their metabolites are discharged to wastewater treatment plants (WWTPs). During wastewater treatment, compounds may be eliminated or degraded into transformation products (TPs) or may be persistent. The aim of this study was to develop an analytical method based on high resolution mass spectrometry (HRMS) for the identification of six psychotropic drugs that are widely consumed in France and present in WWTPs, as well as their potential associated metabolites and TPs. Four out of six psychotropic drugs and between twenty-five and thirty-seven potential TPs were detected in wastewater, although this was based on full scan data. TPs not reported in the literature and specific to the study sites and therefore to the wastewater treatment processes were tentatively identified. For the selected drugs, most known and present TPs were identified, such as desmethylvenlafaxine or norcitalopram. Moreover, the short fragmentation study led rather to the identification of several TPs of carbamazepine as ubiquitous persistent TPs.

Predicting and improving the microbial removal of organic micropollutants during wastewater treatment: A review

Organic micropollutants (OMPs) consist of widely used chemicals such as pharmaceuticals and pesticides that can persist in surface and groundwaters at low concentrations (ng/L to μg/L) for a long time. The presence of OMPs in water can disrupt aquatic ecosystems and threaten the quality of drinking water sources. Wastewater treatment plants (WWTPs) rely on microorganisms to remove major nutrients from water, but their effectiveness at removing OMPs varies. Low removal efficiency might be the result of low concentrations, inherent stable chemical structures of OMPs, or suboptimal conditions in WWTPs. In this review, we discuss these factors, with special emphasis on the ongoing adaptation of microorganisms to degrade OMPs. Finally, recommendations are drawn to improve the prediction of OMP removal in WWTPs and to optimize the design of new microbial treatment strategies. OMP removal seems to be concentration-, compound-, and process-dependent, which poses a great complexity to develop accurate prediction models and effective microbial processes targeting all OMPs.

Avoiding Interferences in Advance: Cyclodextrin Polymers to Enhance Selectivity in Extraction of Organic Micropollutants for Carbon Isotope Analysis

Compound-specific isotope analysis (CSIA) of organic water contaminants can provide important information about their sources and fate in the environment. Analyte enrichment from water remains nonetheless a critical yet inevitable step before measurement. Commercially available solid-phase extraction (SPE) sorbents are inherently nonselective leading to co-extraction of concurrent dissolved organic matter (DOM) and in turn to analytical interferences, especially for low-occurring contaminants. Here, we (i) increased extraction selectivity by synthesizing cyclodextrin polymers (α-, β-, γ-CDP) as SPE sorbents, (ii) assessed their applicability to carbon isotope analysis for a selection of pesticides, and (iii) compared them with commonly used commercial sorbents. Extraction with β-CDP significantly reduced backgrounds in gas chromatography-isotope ratio mass spectrometry (GC-IRMS) and enhanced sensitivity by a factor of 7.5, which was further confirmed by lower carbon-normalized C_DOM/C_analyte ratios in corresponding extracts as derived from dissolved organic carbon (DOC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Gibbs free energies of adsorption demonstrated weak competition between DOM and analyte on the three CDPs. No isotopic fractionation (Δδ¹³C within ± 0.3‰) was observed for the investigated pesticides after using β-CDP as an SPE sorbent covering a range of concentrations (5-500 μg L^-1), flow velocities (5-40 cm min^-1), and sorbent regeneration (up to six times). The present study highlights the benefit of selecting innovative extraction sorbents to avoid interferences in advance. This strategy in combination with existing cleanup approaches offers new prospects for CSIA at field concentrations of tens to hundreds of nanograms per liter.

Special Issue "Microbial Biodegradation and Biotransformation"

The current state of the environment is a major concern [...].

Computational Exploration of Bio-Degradation Patterns of Various Plastic Types

Plastic materials are recalcitrant in the open environment, surviving for longer without complete remediation. The current disposal methods of used plastic material are inefficient; consequently, plastic wastes are infiltrating the natural resources of the biosphere. The mixed composition of urban domestic waste with different plastic types makes them unfavorable for recycling; however, natural assimilation in situ is still an option to explore. In this research work, we have utilized previously published reports on the biodegradation of various plastics types and analyzed the pattern of microbial degradation. Our results demonstrate that the biodegradation of plastic material follows the chemical classification of plastic types based on their main molecular backbone. The clustering analysis of various plastic types based on their biodegradation reports has grouped them into two broad categories of C-C (non-hydrolyzable) and C-X (hydrolyzable). The C-C and C-X groups show a statistically significant difference in their biodegradation pattern at the genus level. The Bacilli class of bacteria is found to be reported more often in the C-C category, which is challenging to degrade compared to C-X. Genus enrichment analysis suggests that Pseudomonas and Bacillus from bacteria and Aspergillus and Penicillium from fungi are potential genera for the bioremediation of mixed plastic waste. The lack of uniformity in reporting the results of microbial degradation of plastic also needs to be addressed to enable productive growth in the field. Overall, the result points towards the feasibility of a microbial-based biodegradation solution for mixed plastic waste.

Understanding the biodegradation pathways of azo dyes by immobilized white-rot fungus, Trametes hirsuta D7, using UPLC-PDA-FTICR MS supported by in silico simulations and toxicity assessment

No biodegradation methods are absolute in the treatment of all textile dyes, which leads to structure-dependent degradation. In this study, biodegradation of three azo dyes, reactive black 5 (RB5), acid blue 113 (AB113), and acid orange 7 (AO7), was investigated using an immobilized fungus, Trametes hirsuta D7. The degraded metabolites were identified using UPLC-PDA-FTICR MS and the biodegradation pathway followed was proposed. RB5 (92%) and AB113 (97%) were effectively degraded, whereas only 30% of AO7 was degraded. Molecular docking simulations were performed to determine the reason behind the poor degradation of AO7. Weak binding affinity, deficiency in H-bonding interactions, and the absence of interactions between the azo (-NN-) group and active residues of the model laccase enzyme were responsible for the low degradation efficiency of AO7. Furthermore, cytotoxicity and genotoxicity assays confirmed that the fungus-treated dye produced non-toxic metabolites. The observations of this study will be useful for understanding and further improving enzymatic dye biodegradation.

Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil

Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.

Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat

In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.

Elucidating the Role of O2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases

Oxygenations of aromatic soil and water contaminants with molecular O₂ catalyzed by Rieske dioxygenases are frequent initial steps of biodegradation in natural and engineered environments. Many of these non-heme ferrous iron enzymes are known to be involved in contaminant metabolism, but the understanding of enzyme–substrate interactions that lead to successful biodegradation is still elusive. Here, we studied the mechanisms of O₂ activation and substrate hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and substrate-specific factors that determine the efficiency of oxygenated product formation. Experiments in enzyme assays of 2-nitrotoluene dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-, fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates reveal that typically 20–100% of the enzyme’s activity involves unproductive paths of O₂ activation with generation of reactive oxygen species through so-called O₂ uncoupling. The ¹⁸O and ¹³C kinetic isotope effects of O₂ activation and nitroaromatic substrate hydroxylation, respectively, suggest that O₂ uncoupling occurs after generation of Fe^III-(hydro)peroxo species in the catalytic cycle. While 2NTDO hydroxylates ortho-substituted nitroaromatic substrates more efficiently, NBDO favors meta-substituted, presumably due to distinct active site residues of the two enzymes. Our data implies, however, that the O₂ uncoupling and hydroxylation activity cannot be assessed from simple structure–reactivity relationships. By quantifying O₂ uncoupling by Rieske dioxygenases, our work provides a mechanistic link between contaminant biodegradation, the generation of reactive oxygen species, and possible adaptation strategies of microorganisms to the exposure of new contaminants.

To be or not to be degraded: in defense of persistence assessment of chemicals

Characterizing the degradation behavior of chemicals in the environment is a key component of chemical hazard and risk assessment. Persistence has been successfully characterized for readily and for slowly degradable chemicals using standardized tests, but for the third group of chemicals with intermediate degradability ("middle group"), the assessment is less straightforward. Whether chemicals of this group behave as persistent or not in a given environment depends on environmental factors such as the presence of sorbents that can limit the bioavailability of chemicals. Uncertainties associated with current persistence assessments of chemicals in the middle group do not imply that persistence assessment is generally inconsistent, too ambiguous for regulatory use, and not useful in chemical hazard and risk assessment. Given the complexity of the environmental factors influencing chemical degradation, and the diversity of commercial chemicals, it has to be accepted though that for chemicals in the middle group even improved testing methods will not remove all of the immanent heterogeneity in their persistence data. For cases with widely different but technically valid persistence data, a weight-of-evidence approach is necessary and the "benefit of the doubt" should follow the precautionary principle in order to protect human and ecosystem health. We maintain that technically valid persistence data, although they might be considered dissatisfying from a scientific point of view because of high variability or even inconclusiveness, can well be sufficient for regulatory purposes. As with anything, also in persistence assessment, the scientific logic aims for a mechanistic description of the processes involved, low uncertainty, and a comprehensive understanding derived from a broad empirical basis. If the scientific logic is used as a benchmark in the regulatory context, this may easily lead to "paralysis by analysis". While regulatory decisions should be based on sound science, discrepancies between scientific goals and regulatory needs and, consequently, different levels of requirements (must-have versus nice-to-have) for degradation studies need to be recognized and appreciated. We further advocate for enhancing consistency between regulatory persistence assessments ("one substance-one assessment"), which is currently not the case.

Synthesizing Laboratory and Field Experiments to Quantify Dominant Transformation Mechanisms of 2,4-Dichlorophenoxyacetic Acid (2,4-D) in Aquatic Environments

Laboratory studies used to assess the environmental fate of organic chemicals such as pesticides fail to replicate environmental conditions, resulting in large errors in predicted transformation rates. We combine laboratory and field data to identify the dominant loss processes of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in lakes for the first time. Microbial and photochemical degradation are individually assessed using laboratory-based microcosms and irradiation studies, respectively. Field campaigns are conducted in six lakes to quantify 2,4-D loss following large-scale herbicide treatments. Irradiation studies show that 2,4-D undergoes direct photodegradation, but modeling efforts demonstrated that this process is negligible under environmental conditions. Microcosms constructed using field inocula show that sediment microbial communities are responsible for degradation of 2,4-D in lakes. Attempts to quantify transformation products are unsuccessful in both laboratory and field studies, suggesting that their persistence is not a major concern. The synthesis of laboratory and field experiments is used to demonstrate best practices in designing laboratory persistence studies and in using those results to mechanistically predict contaminant fate in complex aquatic environments.

Safe and sustainable by design: A computer-based approach to redesign chemicals for reduced environmental hazards

Persistency of chemicals in the environment is seen a pressing issue as it results in accumulation of chemicals over time. Persistent chemicals can be an asset in a well-functioning circular economy where products are more durable and can be reused or recycled. This objective can however not always be fulfilled as release of chemicals from products into the environment can be inherently coupled to their use. In these situations, chemicals should be designed for degradation. In this study, a systematic and computer-aided workflow was developed to facilitate the chemical redesign for reduced persistency. The approach includes elements of Essential Use, Alternatives Assessment and Green and Circular Chemistry and ties into goals recently formulated in the context of the EU Green Deal. The organophosphate chemical triisobutylphosphate (TiBP) was used as a case study for exploration of the approach, as its emission to the environment was expected to be inevitable when used as a flame retardant. Over 6.3 million alternative structures were created in silico and filtered based on QSAR outputs to remove potentially non-readily biodegradable structures. With a multi-criteria analysis based on predicted properties and synthesizability a top 500 of most desirable structures was identified. The target structure (di-n-butyl (2-hydroxyethyl) phosphate) was manually selected and synthesized. The approach can be expanded and further verified to reach its full potential in the mitigation of chemical pollution and to help enable a safe circular economy.

Linking biodegradation kinetics, microbial composition and test temperature - Testing 40 petroleum hydrocarbons using inocula collected in winter and summer

Many factors affect the biodegradation kinetics of chemicals in test systems and the environment. Empirical knowledge is needed on how much test temperature, inoculum, test substances and co-substrates influence the biodegradation kinetics and microbial composition in the test. Water was sampled from the Gudenaa river in winter (2.7 °C) and summer (17 °C) (microbial inoculum) and combined with an aqueous stock solution of >40 petroleum hydrocarbons prepared by passive dosing. This resulted in low-concentration test systems that were incubated for 30 days at 2.7, 12 and 20 °C. Primary biodegradation kinetics, based on substrate depletion relative to abiotic controls, were determined with automated Solid Phase Microextraction coupled to GC/MS. Biodegradation kinetics were remarkably similar for summer and winter inocula when tested at the same temperature, except when cooling summer inoculum to 2.7 °C which delayed degradation relative to winter inoculum. Amplicon sequencing was applied to determine shifts in the microbial composition between season and during incubations: (1) the microbial composition of summer and winter inocula were remarkably similar, (2) the incubation and the incubation temperature had both a clear impact on the microbial composition and (3) the effect of adding >40 petroleum hydrocarbons at low test concentrations was limited but resulted in some proliferation of the known petroleum hydrocarbon degraders Nevskia and Sulfuritalea. Overall, biodegradation kinetics and its temperature dependency were very similar for winter and summer inoculum, whereas the microbial composition was more affected by incubation and test temperature compared to the addition of test chemicals at low concentrations.

Identifying Functional Groups that Determine Rates of Micropollutant Biotransformations Performed by Wastewater Microbial Communities

The goal of this research was to identify functional groups that determine rates of micropollutant (MP) biotransformations performed by wastewater microbial communities. To meet this goal, we performed a series of incubation experiments seeded with four independent wastewater microbial communities and spiked them with a mixture of 40 structurally diverse MPs. We collected samples over time and used high-resolution mass spectrometry to estimate biotransformation rate constants for each MP in each experiment and to propose structures of 46 biotransformation products. We then developed random forest models to classify the biotransformation rate constants based on the presence of specific functional groups or observed biotransformations. We extracted classification importance metrics from each random forest model and compared them across wastewater microbial communities. Our analysis revealed 30 functional groups that we define as either biotransformation promoters, biotransformation inhibitors, structural features that can be biotransformed based on uncharacterized features of the wastewater microbial community, or structural features that are not rate-determining. Our experimental data and analysis provide novel insights into MP biotransformations that can be used to more accurately predict MP biotransformations or to inform the design of new chemical products that may be more readily biodegradable during wastewater treatment.

Toward Characterizing the Genetic Basis of Trace Organic Contaminant Biotransformation in Activated Sludge: The Role of Multicopper Oxidases as a Case Study

Activated sludge treatment leverages the ability of microbes to uptake and (co)-metabolize chemicals and has shown promise in eliminating trace organic contaminants (TrOCs) during wastewater treatment. However, targeted interventions to optimize the process are limited as the fundamental drivers of the observed reactions remain elusive. In this work, we present a comprehensive workflow for the identification and characterization of key enzymes involved in TrOCs biotransformation pathways in complex microbial communities. To demonstrate the applicability of the workflow, we investigated the role of the enzymatic group of multicopper oxidases (MCOs) as one putatively relevant driver of TrOCs biotransformation. To this end, we analyzed activated sludge metatranscriptomic data and selected, synthesized, and heterologously expressed three phylogenetically distinct MCO-encoding genes expressed in communities with different TrOCs oxidation potentials. Following the purification of the encoded enzymes, we screened their activities against different substrates. We saw that MCOs exhibit significant activities against selected TrOCs in the presence of the mediator compound 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid and, in some cases, also in the presence of the wastewater contaminant 4'-hydroxy-benzotriazole. In the first case, we identified oxidation products previously reported from activated sludge communities and concluded that in the presence of appropriate mediators, bacterial MCOs could contribute to the biological removal of TrOCs. Similar investigations of other key enzyme systems may significantly advance our understanding of TrOCs biodegradation and assist the rational design of biology-based water treatment strategies in the future.

Biodegradability, environmental risk assessment and ecological footprint in wastewater technologies for pharmaceutically active compounds removal

Several studies have investigated the removal of pharmaceutically active compounds (PhACs) by wastewater treatment technologies due to the risk that these compounds pose to the environment. In this sense, advanced biological processes have been developed for micropollutants removal, such as membrane bioreactors and moving bed biofilm reactors. Thus, this review holistically evaluated the biodegradation of 18 environmentally hazardous PhACs. Biological processes were assessed including removal efficiencies, environmental risk, and ecological footprint (consumption of resources and energy, atmospheric emissions, and waste generation). The maximum concentration of PhACs for a low or negligible risk scenario in treated wastewater and the potential of biological processes to meet this goal were assessed. Among the evaluated PhACs, the most biodegradable was paracetamol, while the most recalcitrant was diclofenac. Combination of conventional processes and advanced biological processes proved to be the most efficient way to remove several PhACs, mainly the osmotic membrane bioreactor.

Triple-Element Compound-Specific Stable Isotope Analysis (3D-CSIA): Added Value of Cl Isotope Ratios to Assess Herbicide Degradation

Multielement isotope fractionation studies to assess pollutant transformation are well-established for point-source pollution but are only emerging for diffuse pollution by micropollutants like pesticides. Specifically, chlorine isotope fractionation is hardly explored but promising, because many pesticides contain only few chlorine atoms so that "undiluted" position-specific Cl isotope effects can be expected in compound-average data. This study explored combined Cl, N, and C isotope fractionation to sensitively detect biotic and abiotic transformation of the widespread herbicides and groundwater contaminants acetochlor, metolachlor, and atrazine. For chloroacetanilides, abiotic hydrolysis pathways studied under acidic, neutral, and alkaline conditions as well as biodegradation in two soils resulted in pronounced Cl isotope fractionation (ε_Cl from -5.0 ± 2.3 to -6.5 ± 0.7‰). The characteristic dual C-Cl isotope fractionation patterns (Λ_C-Cl from 0.39 ± 0.15 to 0.67 ± 0.08) reveal that Cl isotope analysis provides a robust indicator of chloroacetanilide degradation. For atrazine, distinct Λ_C-Cl values were observed for abiotic hydrolysis (7.4 ± 1.9) compared to previous reports for biotic hydrolysis and oxidative dealkylation (1.7 ± 0.9 and 0.6 ± 0.1, respectively). The 3D isotope approach allowed differentiating transformations that would not be distinguishable based on C and N isotope data alone. This first data set on Cl isotope fractionation in chloroacetanilides, together with new data in atrazine degradation, highlights the potential of using compound-specific chlorine isotope analysis for studying in situ pesticide degradation.